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Winnikoff JR, Milshteyn D, Vargas-Urbano SJ, Pedraza-Joya MA, Armando AM, Quehenberger O, Sodt A, Gillilan RE, Dennis EA, Lyman E, Haddock SHD, Budin I. Homeocurvature adaptation of phospholipids to pressure in deep-sea invertebrates. Science 2024; 384:1482-1488. [PMID: 38935710 DOI: 10.1126/science.adm7607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 05/17/2024] [Indexed: 06/29/2024]
Abstract
Hydrostatic pressure increases with depth in the ocean, but little is known about the molecular bases of biological pressure tolerance. We describe a mode of pressure adaptation in comb jellies (ctenophores) that also constrains these animals' depth range. Structural analysis of deep-sea ctenophore lipids shows that they form a nonbilayer phase at pressures under which the phase is not typically stable. Lipidomics and all-atom simulations identified phospholipids with strong negative spontaneous curvature, including plasmalogens, as a hallmark of deep-adapted membranes that causes this phase behavior. Synthesis of plasmalogens enhanced pressure tolerance in Escherichia coli, whereas low-curvature lipids had the opposite effect. Imaging of ctenophore tissues indicated that the disintegration of deep-sea animals when decompressed could be driven by a phase transition in their phospholipid membranes.
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Affiliation(s)
- Jacob R Winnikoff
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039, USA
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Daniel Milshteyn
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
| | | | | | - Aaron M Armando
- Department of Pharmacology, University of California San Diego Health Sciences, La Jolla, CA 92093, USA
| | - Oswald Quehenberger
- Department of Pharmacology, University of California San Diego Health Sciences, La Jolla, CA 92093, USA
| | - Alexander Sodt
- Unit on Membrane Chemical Physics, National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
| | - Richard E Gillilan
- Center for High-Energy X-ray Sciences, Cornell High Energy Synchrotron Source (CHESS), Ithaca, NY 14850, USA
| | - Edward A Dennis
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
- Department of Pharmacology, University of California San Diego Health Sciences, La Jolla, CA 92093, USA
| | - Edward Lyman
- Department of Physics and Astronomy, University of Delaware, Newark, DE 19716, USA
| | - Steven H D Haddock
- Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039, USA
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Itay Budin
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
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2
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Hata H, Nishiyama M, Kitao A. Molecular dynamics simulation of proteins under high pressure: Structure, function and thermodynamics. Biochim Biophys Acta Gen Subj 2019; 1864:129395. [PMID: 31302180 DOI: 10.1016/j.bbagen.2019.07.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 07/03/2019] [Accepted: 07/08/2019] [Indexed: 12/17/2022]
Abstract
BACKGROUND Molecular dynamics (MD) simulation is well-recognized as a powerful tool to investigate protein structure, function, and thermodynamics. MD simulation is also used to investigate high pressure effects on proteins. For conducting better MD simulation under high pressure, the main issues to be addressed are: (i) protein force fields and water models were originally developed to reproduce experimental properties obtained at ambient pressure; and (ii) the timescale to observe the pressure effect is often much longer than that of conventional MD simulations. SCOPE OF REVIEW First, we describe recent developments in MD simulation methodologies for studying the high-pressure structure and dynamics of protein molecules. These developments include force fields for proteins and water molecules, and enhanced simulation techniques. Then, we summarize recent studies of MD simulations of proteins in water under high pressure. MAJOR CONCLUSIONS Recent MD simulations of proteins in solution under pressure have reproduced various phenomena identified by experiments using high pressure, such as hydration, water penetration, conformational change, helix stabilization, and molecular stiffening. GENERAL SIGNIFICANCE MD simulations demonstrate differences in the properties of proteins and water molecules between ambient and high-pressure conditions. Comparing the results obtained by MD calculations with those obtained experimentally could reveal the mechanism by which biological molecular machines work well in collaboration with water molecules.
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Affiliation(s)
- Hiroaki Hata
- School of Life Science and Technology, Tokyo Institute of Technology, Ookayama, 2-12-1 Meguro-ku, Tokyo 152-8550, Japan
| | - Masayoshi Nishiyama
- Department of Physics, Kindai University, 3-4-1 Kowakae, Higashiosaka, Osaka 577-8502, Japan
| | - Akio Kitao
- School of Life Science and Technology, Tokyo Institute of Technology, Ookayama, 2-12-1 Meguro-ku, Tokyo 152-8550, Japan.
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3
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Pressure effects on collective density fluctuations in water and protein solutions. Proc Natl Acad Sci U S A 2017; 114:11410-11415. [PMID: 29073065 DOI: 10.1073/pnas.1705279114] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Neutron Brillouin scattering and molecular dynamics simulations have been used to investigate protein hydration water density fluctuations as a function of pressure. Our results show significant differences between the pressure and density dependence of collective dynamics in bulk water and in concentrated protein solutions. Pressure-induced changes in the tetrahedral order of the water HB network have direct consequences for the high-frequency sound velocity and damping coefficients, which we find to be a sensitive probe for changes in the HB network structure as well as the wetting of biomolecular surfaces.
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4
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Mori Y, Okamoto Y. Conformational changes of ubiquitin under high pressure conditions: A pressure simulated tempering molecular dynamics study. J Comput Chem 2017; 38:1167-1173. [DOI: 10.1002/jcc.24767] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 01/13/2017] [Accepted: 01/14/2017] [Indexed: 11/12/2022]
Affiliation(s)
- Yoshiharu Mori
- Department of Physics, Graduate School of Science; Nagoya University; Nagoya Aichi 464-8602 Japan
| | - Yuko Okamoto
- Department of Physics, Graduate School of Science; Nagoya University; Nagoya Aichi 464-8602 Japan
- JST-CREST; Nagoya Aichi 464-8602 Japan
- Structural Biology Research Center, Graduate School of Science, Nagoya University; Nagoya Aichi 464-8602 Japan
- Center for Computational Science, Graduate School of Engineering, Nagoya University; Nagoya Aichi 464-8603 Japan
- Information Technology Center, Nagoya University; Nagoya Aichi 464-8601 Japan
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5
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Oshima H, Kinoshita M. Essential roles of protein-solvent many-body correlation in solvent-entropy effect on protein folding and denaturation: Comparison between hard-sphere solvent and water. J Chem Phys 2015; 142:145103. [DOI: 10.1063/1.4917075] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Hiraku Oshima
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Masahiro Kinoshita
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
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6
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Johnson QR, Lindsay RJ, Nellas RB, Fernandez EJ, Shen T. Mapping allostery through computational glycine scanning and correlation analysis of residue-residue contacts. Biochemistry 2015; 54:1534-41. [PMID: 25658131 DOI: 10.1021/bi501152d] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Understanding allosteric mechanisms is essential for the physical control of molecular switches and downstream cellular responses. However, it is difficult to decode essential allosteric motions in a high-throughput scheme. A general two-pronged approach to performing automatic data reduction of simulation trajectories is presented here. The first step involves coarse-graining and identifying the most dynamic residue-residue contacts. The second step is performing principal component analysis of these contacts and extracting the large-scale collective motions expressed via these residue-residue contacts. We demonstrated the method using a protein complex of nuclear receptors. Using atomistic modeling and simulation, we examined the protein complex and a set of 18 glycine point mutations of residues that constitute the binding pocket of the ligand effector. The important motions that are responsible for the allostery are reported. In contrast to conventional induced-fit and lock-and-key binding mechanisms, a novel "frustrated-fit" binding mechanism of RXR for allosteric control was revealed.
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Affiliation(s)
- Quentin R Johnson
- UT-ORNL Graduate School of Genome Science and Technology , Knoxville, Tennessee 37996, United States
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7
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Liu B, Liu Y, Li Y, Wang H, Xu J. An Assessment of Sample Preservation Methods for the Determination of Stable Carbon and Nitrogen Isotope Ratios in Mollusks. ANAL LETT 2013. [DOI: 10.1080/00032719.2013.805415] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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8
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Effect of pressure on the solution structure and hydrogen bond properties of aqueous N-methylacetamide. Chem Phys 2012. [DOI: 10.1016/j.chemphys.2012.09.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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9
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Pressure-induced helix–coil transition of DNA copolymers is linked to water activity. Biophys Chem 2009; 144:62-6. [DOI: 10.1016/j.bpc.2009.06.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2009] [Revised: 06/17/2009] [Accepted: 06/17/2009] [Indexed: 11/18/2022]
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10
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Moussa M, Espinasse V, Perrier-Cornet JM, Gervais P. Pressure treatment of Saccharomyces cerevisiae in low-moisture environments. Appl Microbiol Biotechnol 2009; 85:165-74. [DOI: 10.1007/s00253-009-2126-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2009] [Revised: 07/03/2009] [Accepted: 07/03/2009] [Indexed: 11/29/2022]
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11
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Trzesniak D, Lins RD, van Gunsteren WF. Protein under pressure: Molecular dynamics simulation of the arc repressor. Proteins 2006; 65:136-44. [PMID: 16917942 DOI: 10.1002/prot.21034] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Experimental nuclear magnetic resonance results for the Arc Repressor have shown that this dimeric protein dissociates into a molten globule at high pressure. This structural change is accompanied by a modification of the hydrogen-bonding pattern of the intermolecular beta-sheet: it changes its character from intermolecular to intramolecular with respect to the two monomers. Molecular dynamics simulations of the Arc Repressor, as a monomer and a dimer, at elevated pressure have been performed with the aim to study this hypothesis and to identify the major structural and dynamical changes of the protein under such conditions. The monomer appears less stable than the dimer. However, the complete dissociation has not been seen because of the long timescale needed to observe this phenomenon. In fact, the protein structure altered very little when increasing the pressure. It became slightly compressed and the dynamics of the side-chains and the unfolding process slowed down. Increasing both, temperature and pressure, a tendency of conversion of intermolecular into intramolecular hydrogen bonds in the beta-sheet region has been detected, supporting the mentioned hypothesis. Also, the onset of denaturation of the separated chains was observed.
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Affiliation(s)
- Daniel Trzesniak
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zürich, Zürich, Switzerland
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12
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Harano Y, Kinoshita M. Crucial importance of translational entropy of water in pressure denaturation of proteins. J Chem Phys 2006; 125:24910. [PMID: 16848614 DOI: 10.1063/1.2217011] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We present statistical thermodynamics of pressure denaturation of proteins, in which the three-dimensional integral equation theory is employed. It is applied to a simple model system focusing on the translational entropy of the solvent. The partial molar volume governing the pressure dependence of the structural stability of a protein is expressed for each structure in terms of the excluded volume for the solvent molecules, the solvent-accessible surface area (ASA), and a parameter related to the solvent-density profile formed near the protein surface. It is argued that the entropic effect originating from the translational movement of water molecules plays critical roles in the pressure-induced denaturation. We also show that the exceptionally small size of water molecules among dense liquids in nature is crucial for pressure denaturation. An unfolded structure, which is only moderately less compact than the native structure but has much larger ASA, is shown to turn more stable than the native one at an elevated pressure. The water entropy for the native structure is higher than that for the unfolded structure in the low-pressure region, whereas the opposite is true in the high-pressure region. Such a structure is characterized by the cleft and/or swelling and the water penetration into the interior. In another solvent whose molecular size is 1.5 times larger than that of water, however, the inversion of the stability does not occur any longer. The random coil becomes relatively more destabilized with rising pressure, irrespective of the molecular size of the solvent. These theoretical predictions are in qualitatively good agreement with the experimental observations.
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Affiliation(s)
- Yuichi Harano
- International Innovation Center, Kyoto University, Uji, Kyoto 611-0011, Japan
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13
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Meersman F, Smeller L, Heremans K. Protein stability and dynamics in the pressure–temperature plane. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2006; 1764:346-54. [PMID: 16414316 DOI: 10.1016/j.bbapap.2005.11.019] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2005] [Revised: 11/23/2005] [Accepted: 11/28/2005] [Indexed: 10/25/2022]
Abstract
The pressure-temperature stability diagram of proteins and the underlying assumptions of the elliptical shape of the diagram are discussed. Possible extensions, such as aggregation and fibril formation, are considered. An important experimental observation is the extreme pressure stability of the mature fibrils. Molecular origins of the diagram in terms of models of the partial molar volume of a protein focus on cavities and hydration. Changes in thermal expansivity, compressibility and heat capacity in terms of fluctuations of the enthalpy and volume change of the unfolding should also focus on these parameters. It is argued that the study of water-soluble polymers might further our understanding of the stability diagram. Whereas the role of water in protein behaviour is unquestioned, the role of cavities is less clear.
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Affiliation(s)
- Filip Meersman
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
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14
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Gee P, van Gunsteren W. Numerical Simulation of the Pressure Denaturation of a Helicalβ-Peptide Heptamer Solvated in Methanol. Helv Chim Acta 2006. [DOI: 10.1002/hlca.200690048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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15
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Smolin N, Winter R. A molecular dynamics simulation of SNase and its hydration shell at high temperature and high pressure. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2006; 1764:522-34. [PMID: 16469548 DOI: 10.1016/j.bbapap.2006.01.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2005] [Revised: 12/09/2005] [Accepted: 01/02/2006] [Indexed: 11/19/2022]
Abstract
Temperature- and pressure-induced unfolding of staphylococcal nuclease (SNase) was studied by Royer, Winter et al. using a variety of experimental techniques (SAXS, FT-IR and fluorescence spectroscopy, DSC, PPC, densimetry). For a more detailed understanding of the underlying mechanistic processes of the different unfolding scenarios, we have carried out a series of molecular dynamics (MD) computer simulations on SNase. We investigated the initial changes of the structure of the protein upon application of pressure (up to 5 kbar) and discuss volumetric and structural differences between the native and pressure pre-denatured state. Additionally, we have obtained the compressibility of the protein and hydration water and compare these data with experimental results. As water plays a crucial role in determining the structure, dynamics and function of proteins, we undertook a detailed analysis of the structure of the interfacial water and the protein-solvent H-bond network as well. Moreover, we report here also MD results on the temperature-induced unfolding of SNase. The time evolution of the protein volume and solvent accessible surface area during thermal unfolding have been investigated, and we present a detailed discussion of the temperature-induced unfolding pathway of SNase in terms of secondary and tertiary structural changes.
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Affiliation(s)
- Nikolai Smolin
- Physical Chemistry I-Biophysical Chemistry, Department of Chemistry, University of Dortmund, Otto-Hahn-Str. 6, D-44227 Dortmund, Germany. nikolai.smolin @uni-dortmund.de
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16
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Meersman F, Dobson CM, Heremans K. Protein unfolding, amyloid fibril formation and configurational energy landscapes under high pressure conditions. Chem Soc Rev 2006; 35:908-17. [PMID: 17003897 DOI: 10.1039/b517761h] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
High hydrostatic pressure induces conformational changes in proteins ranging from compression of the molecules to loss of native structure. In this tutorial review we describe how the interplay between the volume change and the compressibility leads to pressure-induced unfolding of proteins and dissociation of amyloid fibrils. We also discuss the effect of pressure on protein folding and free energy landscapes. From a molecular viewpoint, pressure effects can be rationalised in terms of packing and hydration of proteins.
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Affiliation(s)
- Filip Meersman
- Department of Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium.
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17
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Meinhold L, Smith JC. Pressure-dependent transition in protein dynamics at about revealed by molecular dynamics simulation. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2005; 72:061908. [PMID: 16485975 DOI: 10.1103/physreve.72.061908] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2005] [Indexed: 05/06/2023]
Abstract
Molecular dynamics simulations of a crystalline protein, Staphylococcal nuclease, over the pressure range 1 bar to 15 kbar reveal a qualitative change in the internal protein motions at approximately 4 kbar. This change involves the existence of two linear regimes in the mean-square displacement for internal protein motion, <mu2>(P) with a twofold decrease in the slope for P>4 kbar. The major effect of pressure on the dynamics is a loss, with increasing pressure of large amplitude, collective protein modes below 2 THz effective frequency, accompanied by restriction of large-scale solvent translational motion.
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Affiliation(s)
- Lars Meinhold
- Computational Molecular Biophysics, Interdisciplinary Center for Scientific Computing (IWR), University of Heidelberg, Im Neuenheimer Feld 368, D-69120 Heidelberg, Germany
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18
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Meersman F, Smeller L, Heremans K. Extending the Pressure-Temperature State Diagram of Myoglobin. Helv Chim Acta 2005. [DOI: 10.1002/hlca.200590037] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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19
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Canalia M, Malliavin TE, Kremer W, Kalbitzer HR. Molecular dynamics simulations of HPr under hydrostatic pressure. Biopolymers 2004; 74:377-88. [PMID: 15222017 DOI: 10.1002/bip.20089] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The histidine-containing protein (HPr) plays an important role in the phosphotransferase system (PTS). The deformations induced on the protein structure at high hydrostatic pressure values (4, 50, 100, 150, and 200 MPa) were previously (H. Kalbitzer, A. Görler, H. Li, P. Dubovskii, A. Hengstenberg, C. Kowolik, H. Yamada, and K. Akasaka, Protein Science 2000, Vol. 9, pp. 693-703) analyzed by NMR experiments: the nonlinear variations of the amide chemical shifts at high pressure values were supposed to arise from induced shifts in the protein conformational equilibrium. Molecular dynamics (MD) simulations are here performed, to analyze the protein internal mobility at 0.1 MPa, and to relate the nonlinear variations of chemical shifts observed at high pressure, to variations in conformational equilibrium. The global features of the protein structure are only slightly modified along the pressure. Nevertheless, the values of the Voronoi residues volumes show that the residues of alpha-helices are more compressed that those belonging to the beta-sheet. The alpha-helices are also displaying the largest internal mobility and deformation in the simulations. The nonlinearity of the 1H chemical shifts, computed from the MD simulation snapshots, is in qualitative agreement with the nonlinearity of the experimentally observed chemical shifts.
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Affiliation(s)
- Muriel Canalia
- Laboratoire de Biochimie Théorique, CNRS UPR 9080, Institut de Biologie Physico-Chimique, Paris, France
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20
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Wang J, Zhang Z, Liu H, Shi Y. Quasiequilibrium unfolding thermodynamics of a small protein studied by molecular dynamics simulation with an explicit water model. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2003; 67:061903. [PMID: 16241257 DOI: 10.1103/physreve.67.061903] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2003] [Indexed: 05/04/2023]
Abstract
The 124 independent molecular dynamics simulations are completed with total time of 196.8 ns. The calculated unfolding quasiequilibrium thermodynamics of G-IgG-binding domain B1 (GB1) shows the experimentally observed protein transitions: a coil to disordered globule transition, a disordered globule to molten globule transition, a molten globule to nativelike transition, and a nativelike to solidlike state transition. The first protein unfolding phase diagram has been constructed from molecular dynamics simulations with an explicit water model. The calculated melting temperature of GB1 agrees with early experiment. The results also agree with the recent experiment result in which GB1 has more than one intermediate.
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Affiliation(s)
- Jihua Wang
- Department of Physics, De zhou University, De zhou, Shandong, People's Republic of China.
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21
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Meersman F, Heremans K. High pressure induces the formation of aggregation-prone states of proteins under reducing conditions. Biophys Chem 2003; 104:297-304. [PMID: 12834848 DOI: 10.1016/s0301-4622(02)00385-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The pressure stability of ribonuclease A and bovine pancreatic trypsin inhibitor has been investigated with Fourier transform infrared spectroscopy in the presence of the disulfide bond reducing agent 2-mercaptoethanol. The secondary structure of the reduced proteins at high pressure (1 GPa) is not significantly different from the pressure-induced conformation of the native form. Upon decompression under reducing conditions, amorphous aggregates are formed. Such aggregates are not formed upon decompression of the native proteins. Our data demonstrate that high pressure populates, and thus allows the potential characterization of highly aggregation-prone conformations. The relevance of these findings with regard to fibril formation is discussed and the possible role of conformational fluctuations of intermediates on the aggregation pathway is emphasized.
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Affiliation(s)
- Filip Meersman
- Department of Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200D, B-3001 Leuven, Belgium
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22
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Scheyhing CH, Meersman F, Ehrmann MA, Heremans K, Vogel RF. Temperature-pressure stability of green fluorescent protein: a Fourier transform infrared spectroscopy study. Biopolymers 2002; 65:244-53. [PMID: 12382285 DOI: 10.1002/bip.10237] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Green fluorescent protein (GFP) is widely used as a marker in molecular and cell biology. For its use in high-pressure microbiology experiments, its fluorescence under pressure was recently investigated. Changes in fluorescence with pressure were found. To find out whether these are related to structural changes, we investigated the pressure stability of wild-type GFP (wtGFP) and three of its red shift mutants (AFP, GFP(mut1), and GFP(mut2)) using Fourier transform infrared spectroscopy. For the wt GFP, GFP(mut1), and GFP(mut2) we found that up to 13-14 kbar the secondary structure remains intact, whereas AFP starts unfolding around 10 kbar. The 3-D structure is held responsible for this high-pressure stability. Previously observed changes in fluorescence at low pressure are rationalized in terms of the pressure-induced elastic effect. Above 6 kbar, loss of fluorescence is due to aggregation. Revisiting the temperature stability of GFP, we found that an intermediate state is populated along the unfolding pathway of wtGFP. At higher temperatures, the unfolding resulted in the formation of aggregates of wtGFP and its mutants.
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Affiliation(s)
- Carsten H Scheyhing
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, 85350 Freising-Weihenstephan, Germany
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23
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Degraeve P, Rubens P, Lemay P, Heremans K. In situ observation of pressure-induced increased thermostability of two β-galactosidases with FT-IR spectroscopy in the diamond anvil cell. Enzyme Microb Technol 2002. [DOI: 10.1016/s0141-0229(02)00163-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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24
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Meersman F, Smeller L, Heremans K. Comparative Fourier transform infrared spectroscopy study of cold-, pressure-, and heat-induced unfolding and aggregation of myoglobin. Biophys J 2002; 82:2635-44. [PMID: 11964250 PMCID: PMC1302052 DOI: 10.1016/s0006-3495(02)75605-1] [Citation(s) in RCA: 160] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We studied the cold unfolding of myoglobin with Fourier transform infrared spectroscopy and compared it with pressure and heat unfolding. Because protein aggregation is a phenomenon with medical as well as biotechnological implications, we were interested in both the structural changes as well as the aggregation behavior of the respective unfolded states. The cold- and pressure-induced unfolding both yield a partially unfolded state characterized by a persistent amount of secondary structure, in which a stable core of G and H helices is preserved. In this respect the cold- and pressure-unfolded states show a resemblance with an early folding intermediate of myoglobin. In contrast, the heat unfolding results in the formation of the infrared bands typical of intermolecular antiparallel beta-sheet aggregation. This implies a transformation of alpha-helix into intermolecular beta-sheet. H/2H-exchange data suggest that the helices are first unfolded and then form intermolecular beta-sheets. The pressure and cold unfolded states do not give rise to the intermolecular aggregation bands that are typical for the infrared spectra of many heat-unfolded proteins. This suggests that the pathways of the cold and pressure unfolding are substantially different from that of the heat unfolding. After return to ambient conditions the cold- or pressure-treated proteins adopt a partially refolded conformation. This aggregates at a lower temperature (32 degrees C) than the native state (74 degrees C).
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Affiliation(s)
- Filip Meersman
- Department of Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200D, B-3001 Leuven, Belgium
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25
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Hünenberger PH. Calculation of the group-based pressure in molecular simulations. I. A general formulation including Ewald and particle-particle–particle-mesh electrostatics. J Chem Phys 2002. [DOI: 10.1063/1.1463057] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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26
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Abstract
The pressure-temperature phase diagram of various biomolecules is reviewed. Special attention is focused on the elliptic phase diagram of proteins. The phenomenological thermodynamic theory describing this diagram explains the heat, cold and pressure denaturations in a unified picture. The limitations and possible developments of this theory are discussed as well. It is pointed out that a more complex diagram can be obtained when the intermolecular interactions are also taken into account. In this case metastable states appear on the pressure-temperature (p-T) diagram due to intermolecular interactions. Pressure-temperature phase diagrams of other biopolymers are also discussed. While the p-T diagrams of helix-coil transition of nucleic acids and of gel-liquid crystal transition of lipid bilayers are non-elliptical, those of gelatinization of starch and of phase separation of some synthetic polymers show an elliptic profile, similar to that of proteins. Finally, the p-T diagram of bacterial inactivation is shown to be elliptic. From the point of view of basic science, this fact shows that the key factor of inactivation should be the protein type, and from the viewpoint of practical applications, it serves as the theoretical basis of pressure treatment of biosystems.
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Affiliation(s)
- László Smeller
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary.
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27
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Abstract
Pressure is a thermodynamic variable which is particularly suitable for exploration of the properties of biological macromolecules. For proteins, in particular, denaturation induced by pressure is different from that induced by temperature or denaturants. The response of proteins to pressure changes can provide information on properties of their native and non-native states. This review focuses on molecular dynamics studies of the effect of pressure on detailed atomic models of proteins. It also reports on other theoretical approaches, such as Monte Carlo simulations, which have been used to study simplified models. Another purpose of this review is to try to point out potential future studies that may be both interesting and feasible, with constantly increasing computing power.
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Affiliation(s)
- Emanuele Paci
- Laboratoire de Chimie Biophysique, ISIS, Université Louis Pasteur, Strasbourg, France.
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28
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Lynch TW, Sligar SG. Experimental and theoretical high pressure strategies for investigating protein-nucleic acid assemblies. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1595:277-82. [PMID: 11983402 DOI: 10.1016/s0167-4838(01)00350-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A method was developed to investigate the stability of protein-nucleic acid complexes using hydrostatic pressure during electrophoretic gel mobility shift analysis. The initial system probed by this technique was the well-characterized cognate BamHI-DNA complex. Band shift analysis at several elevated pressures found the equilibrium dissociation (K(d)) constant to be dependent on pressure, which allowed the volume change of dissociation (deltaV) to be calculated. In order to describe the effects of pressure on the specific BamHI-DNA complex at the molecular level, molecular dynamics simulations at both ambient and elevated pressure was performed. Comparison of the simulation trajectories identified several individual BamHI-DNA contacts that are disrupted due to pressure. The disruption of these contacts can be attributed to an observed pressure-induced increase in hydration at the protein-DNA interface during the elevated pressure simulation.
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Affiliation(s)
- T W Lynch
- Department of Biochemistry, University of Illinois, Urbana, IL 61801, USA
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29
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Balny C, Masson P, Heremans K. High pressure effects on biological macromolecules: from structural changes to alteration of cellular processes. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1595:3-10. [PMID: 11983383 DOI: 10.1016/s0167-4838(01)00331-4] [Citation(s) in RCA: 205] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Claude Balny
- INSERM Unité 128, IFR 24, CNRS, 1919, route de Mende, Montpellier, France.
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30
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High pressure bioscience and biotechnology: A century and a decade perspective. ACTA ACUST UNITED AC 2002. [DOI: 10.1016/s0921-0423(02)80072-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
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31
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Mentré P, Hui Bon Hoa G. Effects of high hydrostatic pressures on living cells: a consequence of the properties of macromolecules and macromolecule-associated water. INTERNATIONAL REVIEW OF CYTOLOGY 2001; 201:1-84. [PMID: 11057830 DOI: 10.1016/s0074-7696(01)01001-4] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Sixty percent of the Earth's biomass is found in the sea, at depths greater than 1000 m, i.e., at hydrostatic pressures higher than 100 atm. Still more surprising is the fact that living cells can reversibly withstand pressure shifts of 1000 atm. One explanation lies in the properties of cellular water. Water forms a very thin film around macromolecules, with a heterogeneous structure that is an image of the heterogeneity of the macromolecular surface. The density of water in contact with macromolecules reflects the physical properties of their different domains. Therefore, any macromolecular shape variations involving the reorganization of water and concomitant density changes are sensitive to pressure (Le Chatelier's principle). Most of the pressure-induced changes to macromolecules are reversible up to 2000 atm. Both the effects of pressure shifts on living cells and the characteristics of pressure-adapted species are opening new perspectives on fundamental problems such as regulation and adaptation.
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Affiliation(s)
- P Mentré
- Station INRA 806, Institut de Biologie Physico-Chimique, Paris, France
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32
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Eastman P, Grønbech-Jensen N, Doniach S. Simulation of protein folding by reaction path annealing. J Chem Phys 2001. [DOI: 10.1063/1.1342162] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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33
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Marchi M, Akasaka K. Simulation of Hydrated BPTI at High Pressure: Changes in Hydrogen Bonding and Its Relation with NMR Experiments. J Phys Chem B 2000. [DOI: 10.1021/jp002539p] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Massimo Marchi
- Section de Biophysique des Protéines et des Membranes, DBCM, DSV, CEA, Centre d'Études, Saclay, 91191 Gif-sur-Yvette Cedex, France
| | - Kazuyuki Akasaka
- Department of Molecular Science, Graduate School of Science and Technology, Kobe University, Kobe 657-8501, Japan
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34
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Onuchic JN, Nymeyer H, García AE, Chahine J, Socci ND. The energy landscape theory of protein folding: insights into folding mechanisms and scenarios. ADVANCES IN PROTEIN CHEMISTRY 2000; 53:87-152. [PMID: 10751944 DOI: 10.1016/s0065-3233(00)53003-4] [Citation(s) in RCA: 195] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- J N Onuchic
- Department of Physics, University of California at San Diego, La Jolla 92093-0319, USA
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35
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Chai CC, Jhon MS. Molecular Dynamics Study on Protein and it's Water Structure at High Pressure. MOLECULAR SIMULATION 2000. [DOI: 10.1080/08927020008025372] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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36
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Li H, Yamada H, Akasaka K. Effect of pressure on the tertiary structure and dynamics of folded basic pancreatic trypsin inhibitor. Biophys J 1999; 77:2801-12. [PMID: 10545378 PMCID: PMC1300552 DOI: 10.1016/s0006-3495(99)77112-2] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
The on-line high-pressure cell NMR technique was used to study pressure-induced changes in the tertiary structure and dynamics of a globular protein, basic pancreatic trypsin inhibitor (BPTI). Practically all the proton signals of BPTI were observed with (1)H two-dimensional NMR spectroscopy at 750 MHz at variable pressure between 1 and 2000 bar. Chemical shifts, nuclear Overhauser effect (NOE), and line shapes were used to analyze conformational and dynamic changes of the protein as functions of pressure. Linear, reversible, but nonuniform pressure-induced chemical shift changes of practically all the C(alpha) protons and side chain protons showed that the entire secondary and tertiary structures are altered by pressure within the folded ensemble of BPTI. The high field shift tendency of most side chain proton signals and the increase in NOE intensities of some specific side chain protons indicated a site-specific compaction of the tertiary structure. Pressure dependence of ring flip rates was deduced from resonance line shapes of the slices of the two-dimensional NMR spectrum for ring proton signals of Tyr-35 and Phe-45. The rates of the flip-flop motions were considerably reduced at high pressure, from which activation volumes were determined to be 85 +/- 20 A(3) (or 51.2 ml/mol) and 46 +/- 9 A(3) (or 27.7 ml/mol) for Tyr-35 and Phe-45, respectively, at 57 degrees C. The present experiments confirm that pressure affects the entire secondary and tertiary structures of a globular protein with specific compaction of a core, leading to quite significant changes in slow internal dynamics of a globular protein.
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Affiliation(s)
- H Li
- Department of Chemistry, Faculty of Science, Kobe University, Kobe 657-8501, Japan
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37
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Akasaka K, Li H, Yamada H, Li R, Thoresen T, Woodward CK. Pressure response of protein backbone structure. Pressure-induced amide 15N chemical shifts in BPTI. Protein Sci 1999; 8:1946-53. [PMID: 10548039 PMCID: PMC2144150 DOI: 10.1110/ps.8.10.1946] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The effect of pressure on amide 15N chemical shifts was studied in uniformly 15N-labeled basic pancreatic trypsin inhibitor (BPTI) in 90%1H2O/10%2H2O, pH 4.6, by 1H-15N heteronuclear correlation spectroscopy between 1 and 2,000 bar. Most 15N signals were low field shifted linearly and reversibly with pressure (0.468 +/- 0.285 ppm/2 kbar), indicating that the entire polypeptide backbone structure is sensitive to pressure. A significant variation of shifts among different amide groups (0-1.5 ppm/2 kbar) indicates a heterogeneous response throughout within the three-dimensional structure of the protein. A tendency toward low field shifts is correlated with a decrease in hydrogen bond distance on the order of 0.03 A/2 kbar for the bond between the amide nitrogen atom and the oxygen atom of either carbonyl or water. The variation of 15N shifts is considered to reflect site-specific changes in phi, psi angles. For beta-sheet residues, a decrease in psi angles by 1-2 degrees/2 kbar is estimated. On average, shifts are larger for helical and loop regions (0.553 +/- 0.343 and 0.519 +/- 0.261 ppm/2 kbar, respectively) than for beta-sheet (0.295 +/- 0.195 ppm/2 kbar), suggesting that the pressure-induced structural changes (local compressibilities) are larger in helical and loop regions than in beta-sheet. Because compressibility is correlated with volume fluctuation, the result is taken to indicate that the volume fluctuation is larger in helical and loop regions than in beta-sheet. An important aspect of the volume fluctuation inferred from pressure shifts is that they include motions in slower time ranges (less than milliseconds) in which many biological processes may take place.
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Affiliation(s)
- K Akasaka
- Department of Molecular Science, The Graduate School of Science and Technology, Kobe University, Japan.
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38
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Heremans K, Smeller L. Protein structure and dynamics at high pressure. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1386:353-70. [PMID: 9733996 DOI: 10.1016/s0167-4838(98)00102-2] [Citation(s) in RCA: 334] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The effect of pressure on the structure and dynamics of proteins is discussed in the framework of the pressure-temperature stability phase diagram. The elastic (reversible) properties, thermal expansion, compressibility and heat capacity, are correlated with the entropy, volume, and the coupling between entropy and volume fluctuations respectively. The experimental approaches that can be used to measure these quantities are reviewed. The plastic (conformational) changes reflect the changes in these properties in the cold, pressure and heat denaturation.
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Affiliation(s)
- K Heremans
- Department of Chemistry, Katholieke Universiteit Leuven, Belgium.
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39
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Hummer G, Garde S, García AE, Paulaitis ME, Pratt LR. The pressure dependence of hydrophobic interactions is consistent with the observed pressure denaturation of proteins. Proc Natl Acad Sci U S A 1998; 95:1552-5. [PMID: 9465053 PMCID: PMC19087 DOI: 10.1073/pnas.95.4.1552] [Citation(s) in RCA: 499] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Proteins can be denatured by pressures of a few hundred MPa. This finding apparently contradicts the most widely used model of protein stability, where the formation of a hydrophobic core drives protein folding. The pressure denaturation puzzle is resolved by focusing on the pressure-dependent transfer of water into the protein interior, in contrast to the transfer of nonpolar residues into water, the approach commonly taken in models of protein unfolding. Pressure denaturation of proteins can then be explained by the pressure destabilization of hydrophobic aggregates by using an information theory model of hydrophobic interactions. Pressure-denatured proteins, unlike heat-denatured proteins, retain a compact structure with water molecules penetrating their core. Activation volumes for hydrophobic contributions to protein folding and unfolding kinetics are positive. Clathrate hydrates are predicted to form by virtually the same mechanism that drives pressure denaturation of proteins.
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Affiliation(s)
- G Hummer
- Theoretical Division, MS K710, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
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40
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Fusi P, Goossens K, Consonni R, Grisa M, Puricelli P, Vecchio G, Vanoni M, Zetta L, Heremans K, Tortora P. Extreme heat- and pressure-resistant 7-kDa protein P2 from the archaeon Sulfolobus solfataricus is dramatically destabilized by a single-point amino acid substitution. Proteins 1997; 29:381-90. [PMID: 9365992 DOI: 10.1002/(sici)1097-0134(199711)29:3<381::aid-prot11>3.0.co;2-j] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
This study reports the characterization of the recombinant 7-kDa protein P2 from Sulfolobus solfataricus and the mutants F31A and F31Y with respect to temperature and pressure stability. As observed in the NMR, FTIR, and CD spectra, wild-type protein and mutants showed substantially similar structures under ambient conditions. However, midpoint transition temperatures of the denaturation process were 361, 334, and 347 K for wild type, F31A, and F31Y mutants, respectively: thus, alanine substitution of phenylalanine destabilized the protein by as much as 27 K. Midpoint transition pressures for wild type and F31Y mutant could not be accurately determined because they lay either beyond (wild type) or close to (F31Y) 14 kbar, a pressure at which water undergoes a phase transition. However, a midpoint transition pressure of 4 kbar could be determined for the F31A mutant, implying a shift in transition of at least 10 kbar. The pressure-induced denaturation was fully reversible; in contrast, thermal denaturation of wild type and mutants was only partially reversible. To our knowledge, both the pressure resistance of protein P2 and the dramatic pressure and temperature destabilization of the F31A mutant are unprecedented. These properties may be largely accounted for by the role of an aromatic cluster where Phe31 is found at the core, because interactions among aromatics are believed to be almost pressure insensitive; furthermore, the alanine substitution of phenylalanine should create a cavity with increased compressibility and flexibility, which also involves an impaired pressure and temperature resistance.
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Affiliation(s)
- P Fusi
- Dipartimento di Fisiologia e Biochimica generali, Università di Milano, Italy
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